AMBER Archive (2009)

Subject: Re: [AMBER] Influence about HIS-HIE-HIS-HIP

From: Rilei Yu (yulaomao1983_at_yahoo.com.cn)
Date: Thu Apr 30 2009 - 19:37:17 CDT

Dear David,
 
You really told me an very useful website. Thanks fo your help!
 
Best Regards,

Rilei Yu

--- 09年4月30日，周四, David A. Case <case_at_biomaps.rutgers.edu> 写道：

发件人: David A. Case <case_at_biomaps.rutgers.edu>
主题: Re: [AMBER] Influence about HIS-HIE-HIS-HIP
收件人: "AMBER Mailing List" <amber_at_ambermd.org>
日期: 2009年4月30日,周四,下午10:27

On Thu, Apr 30, 2009, Rilei Yu wrote:
>
>  
> It is known that the default "leaprc" files assign the name HIS to
> HIE. I donot know wheather this change will introduce great influence
> to my MD simulation or not. You know an HIS is in the ligand binding
> pocket. So I believe there should be some influence to my protein
> complex simulation. Is there any tutorial than can guide me to assign
> the right from to the HIS. Namely, when will the HIS be use default
> form, and when will it be used as other forms such as HIP and HID?

The molprobity or reduce programs from Duke can help with this, as can several
programs on the web which are designed to predict pKa's of residues.  You
might want to look at H++ (although other sites carry out similar
calculations):

  http://biophysics.cs.vt.edu/H++/

...dac

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